SAXSdb — 1bd3

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1. Protein Identity and Related Structures Protein Identity & Related Structures

URACIL PHOSPHORIBOSYLTRANSFERASE

Toxoplasma gondii

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–244 Chain B； UniProt 2–244 Chain C； UniProt 2–244 Chain D； UniProt 2–244	Mutation：C128V	PO4 PHOSPHATE ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.93 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1BD3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BD4 UPRT-URACIL COMPLEX Deposited 1998-05-12	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–244（243 aa） Chain B 2–244（243 aa） Chain C 2–244（243 aa） Chain D 2–244（243 aa）	Mutation：C128V Mutation：C128V Mutation：C128V Mutation：C128V	PO4 PHOSPHATE ION × 8 URA URACIL × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1JLR STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE GTP COMPLEX 2 MUTANT C128V Deposited 2001-07-16	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–244（243 aa） Chain B 2–244（243 aa） Chain C 2–244（243 aa） Chain D 2–244（243 aa）	Mutation：C1128V Mutation：C1128V Mutation：C1128V Mutation：C1128V	PO4 PHOSPHATE ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；278 K；Citrate buffer, NaCl, Ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.45 Å R-free 0.242
1JLS STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE URACIL/CPR 2 MUTANT C128V Deposited 2001-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–244（243 aa） Chain B 2–244（243 aa） Chain C 2–244（243 aa） Chain D 2–244（243 aa）	Mutation：C128V Mutation：C128V Mutation：C128V Mutation：C128V	PO4 PHOSPHATE ION × 9 MG MAGNESIUM ION × 1 URA URACIL × 4 PRP 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；NaCl, citrate/phosphate buffer, PEG 3400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.288
1UPF STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE, MUTANT C128V BOUND TO THE DRUG 5-FLUOROURACIL Deposited 1998-06-17	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 21–244（224 aa） Chain B 21–244（224 aa） Chain C 21–244（224 aa） Chain D 21–244（224 aa）	Mutation：C128V Mutation：C128V Mutation：C128V Mutation：C128V	SO4 SULFATE ION × 12 URF 5-FLUOROURACIL × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1UPU STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE, MUTANT C128V, BOUND TO PRODUCT URIDINE-1-MONOPHOSPHATE (UMP) Deposited 1998-04-16	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 21–244（224 aa） Chain B 21–244（224 aa） Chain C 21–244（224 aa） Chain D 21–244（224 aa）	Mutation：C128V Mutation：C128V Mutation：C128V Mutation：C128V	PO4 PHOSPHATE ION × 4 U5P URIDINE-5'-MONOPHOSPHATE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UPP_TOXGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–243； UniProt 2–244 Author chain B； PDBConstruct 1–243； UniProt 2–244 Author chain C； PDBConstruct 1–243； UniProt 2–244 Author chain D； PDBConstruct 1–243； UniProt 2–244

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bd3
Deposition date deposition_date	1998-05-12
Structure title title	STRUCTURE OF THE APO URACIL PHOSPHORIBOSYLTRANSFERASE, 2 MUTANT C128V
Keywords keywords	TRANSFERASE, GLYCOSYLTRANSFERASE, UPRTASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.61 Å
Radius of gyration Rg (electron density) rg_electron	28.35 Å
Forward intensity I(0) i0	161397000.00
Molecular weight molecular_weight	102810.0 kDa
Excluded volume excluded_volume	130010 Å³
Envelope volume envelope_volume	157720 Å³
Hydration-shell volume shell_volume	44201 Å³
Envelope diameter envelope_diameter	111.1 Å
Shell Rg shell_rg	37.43 Å
Envelope Rg envelope_rg	28.55 Å
Shape Rg shape_rg	28.35 Å
Total Rg total_rg	29.22 Å
Total atoms total_atoms	7192
Residues n_residues	896
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	106.6 Å
Rg (real space) rg_real	29.45 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	1.6140e+08
I(0) uncertainty (real space) i0_real_error	2.3710e+06
Rg (reciprocal space) rg_reciprocal	29.52 Å
I(0) (reciprocal space) i0_reciprocal	161400000.0000
Solution quality estimate total_estimate	0.8406
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	37.5 Å
Skewness Skewness skewness	0.175
Kurtosis Kurtosis kurtosis	-0.311
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	58290000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.647; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	URACIL PHOSPHORIBOSYLTRANSFERASE
Molecular weight formula_weight	27558.2 kDa
EC 编号 ec_number	2.4.2.9
Mutation mutation	C128V
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C,B,A
Atom count atom_count	7604

AQVPASGKLLVDPRYSTNDQEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFQKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGVRIGKILIQRDETTAEPKLIYEKLPADIRERWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM

来源 Source

来源生物 organism	Toxoplasma gondii
NCBI Class编号 ncbi_taxonomy_id	5811
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	412

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1bd3a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1bd3b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1bd3c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1bd3d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

CATH v4.4 (4 domains)

Domain ID domain_id	1bd3A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1bd3B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1bd3C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1bd3D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

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8. Citations (1)

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Unit-cell length a length_a	60.600 Å
Unit-cell length b length_b	141.690 Å
Unit-cell length c length_c	71.370 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1860
R_free r_free	—

fit	/app/data/saxs_computation/bd/1bd3/1bd3.fit
pddf	/app/data/pr_computation/bd/1bd3/1bd3.pr.out
profile	/app/data/saxs_computation/bd/1bd3/1bd3.dat

STRUCTURE OF THE APO URACIL PHOSPHORIBOSYLTRANSFERASE, 2 MUTANT C128V

1. Protein Identity and Related Structures Protein Identity & Related Structures

URACIL PHOSPHORIBOSYLTRANSFERASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction